LAMMPS (27 Nov 2018)
  using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide

units		real
atom_style	full

pair_style	lj/charmm/coul/long 8.0 10.0 10.0
bond_style      harmonic
angle_style     charmm
dihedral_style  charmm
improper_style  harmonic
kspace_style	pppm 0.0001

read_data	data.peptide
  orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
  1 by 2 by 2 MPI processor grid
  reading atoms ...
  2004 atoms
  reading velocities ...
  2004 velocities
  scanning bonds ...
  3 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  14 = max dihedrals/atom
  scanning impropers ...
  1 = max impropers/atom
  reading bonds ...
  1365 bonds
  reading angles ...
  786 angles
  reading dihedrals ...
  207 dihedrals
  reading impropers ...
  12 impropers
  4 = max # of 1-2 neighbors
  7 = max # of 1-3 neighbors
  14 = max # of 1-4 neighbors
  18 = max # of special neighbors

neighbor	2.0 bin
neigh_modify	delay 5

timestep	2.0

group		peptide type <= 12
84 atoms in group peptide
group		one id 2 4 5 6
4 atoms in group one
group		two id 80 82 83 84
4 atoms in group two
group		ref id 37
1 atoms in group ref
group		colvar union one two ref
9 atoms in group colvar

fix		1 all nvt temp  275.0 275.0 100.0 tchain 1

fix		3  one spring couple two 100.0 0.0 0.0 0.0 10.0

fix		4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
  19 = # of size 2 clusters
  6 = # of size 3 clusters
  3 = # of size 4 clusters
  640 = # of frozen angles

#dump		1 colvar custom 1 dump.spring2.lammpstrj id xu yu zu fx fy fz
#dump_modify 1  sort id

thermo_style	custom step temp etotal pe ke epair ebond f_3
thermo		10


run		100
PPPM initialization ...
  using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
  G vector (1/distance) = 0.268725
  grid = 15 15 15
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0228209
  estimated relative force accuracy = 6.87243e-05
  using double precision FFTs
  3d grid and FFT values/proc = 4312 960
Neighbor list info ...
  update every 1 steps, delay 5 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 12
  ghost atom cutoff = 12
  binsize = 6, bins = 5 5 5
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/charmm/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
SHAKE stats (type/ave/delta) on step 0
  4 1.111 1.44264e-05
  6 0.996998 7.26967e-06
  8 1.08 1.32536e-05
  10 1.111 1.22749e-05
  12 1.08 1.11767e-05
  14 0.96 0
  18 0.957206 4.37979e-05
  31 104.519 0.00396029
Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond f_3 
       0    282.10052    -5237.458   -6372.3766    1134.9186    -6442.768    16.557152    273.74323 
      10    333.47919   -4982.3968   -6324.0169    1341.6201   -6400.4223    21.367762    12.393263 
      20    309.56902   -4999.4978   -6244.9249    1245.4271   -6401.6981     43.59542    13.004314 
      30     316.9763   -5025.5662   -6300.7935    1275.2273   -6422.5375    27.323196    6.7589585 
      40    297.55779   -5088.2204   -6285.3252    1197.1047    -6395.375      13.6769    25.625024 
      50    296.79994   -5117.2966   -6311.3525    1194.0558   -6451.8309    30.631241    5.3320863 
      60    281.72778   -5188.4969   -6321.9159     1133.419   -6427.8856    26.287723    20.574037 
      70    277.26053   -5224.8434   -6340.2902    1115.4468   -6447.8521    27.742893   0.69420283 
      80    268.01484   -5281.8509   -6360.1014    1078.2505   -6496.6086    20.300754    5.2607186 
      90    270.43472   -5334.0835   -6422.0694    1087.9859   -6563.2511    39.846095    1.1832272 
SHAKE stats (type/ave/delta) on step 100
  4 1.11096 0.000191462
  6 0.996989 3.55508e-05
  8 1.08 9.0997e-06
  10 1.111 1.58544e-05
  12 1.08 5.80604e-06
  14 0.959997 0
  18 0.957198 2.92445e-05
  31 104.52 0.00239923
     100    260.35636   -5387.2284   -6434.6681    1047.4397   -6534.1956    20.246866  0.075048487 
Loop time of 0.616036 on 4 procs for 100 steps with 2004 atoms

Performance: 28.050 ns/day, 0.856 hours/ns, 162.328 timesteps/s
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.40372    | 0.41244    | 0.41714    |   0.8 | 66.95
Bond    | 0.00053573 | 0.0011384  | 0.0017946  |   1.8 |  0.18
Kspace  | 0.060087   | 0.063993   | 0.07306    |   2.1 | 10.39
Neigh   | 0.1033     | 0.10349    | 0.1036     |   0.0 | 16.80
Comm    | 0.01568    | 0.016453   | 0.017178   |   0.5 |  2.67
Output  | 0.00028253 | 0.00032026 | 0.00043178 |   0.0 |  0.05
Modify  | 0.016238   | 0.016955   | 0.017704   |   0.5 |  2.75
Other   |            | 0.001239   |            |       |  0.20

Nlocal:    501 ave 513 max 494 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Nghost:    6572.5 ave 6593 max 6548 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs:    177058 ave 181778 max 174301 min
Histogram: 2 0 0 0 1 0 0 0 0 1

Total # of neighbors = 708234
Ave neighs/atom = 353.41
Ave special neighs/atom = 2.34032
Neighbor list builds = 13
Dangerous builds = 1
Total wall time: 0:00:00
